A personal knowledge base for polymer simulation resources, papers, tutorials, scripts, tools, and code.
This repository is intended to organize practical notes and reusable materials for polymer simulation work, including molecular dynamics workflows, force fields, analysis scripts, literature notes, and tool references.
papers/- literature notes, reading lists, and citation collections.tutorials/- step-by-step workflows and learning notes.scripts/- reusable scripts for setup, simulation, analysis, and visualization.tools/- notes about software, packages, utilities, and configuration.code/- project code, prototypes, and reproducible examples.resources/- links, datasets, templates, and miscellaneous references.
- Polymer molecular dynamics
- Coarse-grained and atomistic models
- Force field selection and parameterization
- LAMMPS, GROMACS, RadonPy, and related tools
- Structure generation and equilibration workflows
- Trajectory analysis and property prediction
- Reproducible simulation pipelines
Keep entries concise, reproducible, and source-linked whenever possible. For scripts and code, include basic usage notes and dependencies near the file.